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Pharmacological Chaperoning in Human alpha-Galactosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HG5 PDB ENTRY 3HG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 293 8-15% PEG 8000, 0.1 M Sodium Cacodylate, 0.02 M Magnesium Chloride, pH 5.1, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.813 α = 90 b = 182.635 β = 90 c = 47.73 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 TOROIDAL FOCUSING MIRROR 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.000 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 50 95 0.095 8.3 6.2 66778 40.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 92.4 0.816 5.8 6394
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3HG5 2.105 30.44 66564 3360 94.48 0.1954 0.1936 0.1911 0.2299 0.2284 RANDOM 38.3445
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.7 0.31 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 14.117 r_dihedral_angle_3_deg 13.369 r_scangle_it 8.098 r_dihedral_angle_1_deg 5.65 r_scbond_it 5.37 r_mcangle_it 3.486 r_mcbond_it 2.161 r_angle_refined_deg 1.126 r_mcbond_other 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.459 r_dihedral_angle_4_deg 14.117 r_dihedral_angle_3_deg 13.369 r_scangle_it 8.098 r_dihedral_angle_1_deg 5.65 r_scbond_it 5.37 r_mcangle_it 3.486 r_mcbond_it 2.161 r_angle_refined_deg 1.126 r_mcbond_other 0.825 r_angle_other_deg 0.818 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6253 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 403
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction AMoRE phasing